Wrap Rmarkdown md_output table chunk output in code chunks - r

Question

I want my Rmarkdown, when converted to .md, text chunk output to be wrapped in code ticks (``` * ```).
For example as it is now, an Rmarkdown document like so:
---
title: 'This is a test title'
date: '`r Sys.Date()`'
output:
md_document:
variant: commonmark #or gfm
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(
echo = TRUE,
message = FALSE,
warning = FALSE
)
```
```{r echo=FALSE}
library(palmerpenguins)
```
```{r echo=TRUE}
penguins
```
This is some text.
Rendered with rmarkdown::render("path/to/test.Rmd") to:
```
penguins
```
## # A tibble: 344 × 8
## species island bill_le…¹ bill_…² flipp…³ body_…⁴ sex year
## <fct> <fct> <dbl> <dbl> <int> <int> <fct> <int>
## 1 Adelie Torgersen 39.1 18.7 181 3750 male 2007
## 2 Adelie Torgersen 39.5 17.4 186 3800 fema… 2007
## 3 Adelie Torgersen 40.3 18 195 3250 fema… 2007
## 4 Adelie Torgersen NA NA NA NA <NA> 2007
## 5 Adelie Torgersen 36.7 19.3 193 3450 fema… 2007
## 6 Adelie Torgersen 39.3 20.6 190 3650 male 2007
## 7 Adelie Torgersen 38.9 17.8 181 3625 fema… 2007
## 8 Adelie Torgersen 39.2 19.6 195 4675 male 2007
## 9 Adelie Torgersen 34.1 18.1 193 3475 <NA> 2007
## 10 Adelie Torgersen 42 20.2 190 4250 <NA> 2007
## # … with 334 more rows, and abbreviated variable names
## # ¹​bill_length_mm, ²​bill_depth_mm, ³​flipper_length_mm,
## # ⁴​body_mass_g
This is some text.
How do you get the table (penguins) that is output in the .md document to be wrapped in code ticks (```)?
At the moment, I can get it to work if I use:
---
output:
html_document:
keep_md: TRUE
---
In this example the .md that is generated and kept has all text output surrounded by code ticks. How do I get this without writing an html document?
I've tried updating the s3 object knit_print() but can't figure out how to get it to work. I've also tried various flavors of markdown and looked at pandoc add ons but can't figure it out. I've been googling for hours please help.

Answer 1

A simple approach is to provide a class to class.output chunk option, then the chunk output will be wrapped inside codeticks (triple backticks) automatically.
And to have this behavior for all output, add class.output="output" to knitr::opts_chunk$set.
---
title: 'This is a test title'
date: '`r Sys.Date()`'
output:
md_document:
variant: commonmark #or gfm
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(
echo = TRUE,
message = FALSE,
warning = FALSE,
class.output="output"
)
```
```{r echo=FALSE}
library(palmerpenguins)
```
```{r echo=TRUE}
penguins
```
```{r}
1 + 1
```
This is some text.
md output
``` r
penguins
```
``` output
## # A tibble: 344 × 8
## species island bill_length_mm bill_depth_mm flipper_…¹ body_…² sex year
## <fct> <fct> <dbl> <dbl> <int> <int> <fct> <int>
## 1 Adelie Torgersen 39.1 18.7 181 3750 male 2007
## 2 Adelie Torgersen 39.5 17.4 186 3800 fema… 2007
## 3 Adelie Torgersen 40.3 18 195 3250 fema… 2007
## 4 Adelie Torgersen NA NA NA NA <NA> 2007
## 5 Adelie Torgersen 36.7 19.3 193 3450 fema… 2007
## 6 Adelie Torgersen 39.3 20.6 190 3650 male 2007
## 7 Adelie Torgersen 38.9 17.8 181 3625 fema… 2007
## 8 Adelie Torgersen 39.2 19.6 195 4675 male 2007
## 9 Adelie Torgersen 34.1 18.1 193 3475 <NA> 2007
## 10 Adelie Torgersen 42 20.2 190 4250 <NA> 2007
## # … with 334 more rows, and abbreviated variable names ¹​flipper_length_mm,
## # ²​body_mass_g
```
``` r
1 + 1
```
``` output
## [1] 2
```
This is some text.

Answer 2

Feels a bit hacky, but you can cat the backticks as output to code chunks, but drop the comment symbol (##). (I'm using four backticks for the code blocks below to get the syntax highlighting correct)
````{r echo=FALSE, comment=NA}
cat('```')
````
````{r echo=FALSE}
penguins
````
````{r echo=FALSE, comment=NA}
cat('```')
````